Regression Calibration (RC) google
Medical studies that depend on electronic health records (EHR) data are often subject to measurement error as the data are not collected to support research questions under study. Methodology to address covariate measurement error has been well developed; however, time-to-event error has also been shown to cause significant bias but methods to address it are relatively underdeveloped. More generally, it is possible to observe errors in both the covariate and the time-to-event outcome that are correlated. We propose regression calibration (RC) estimators to simultaneously address correlated error in the covariates and the censored event time. Although RC can perform well in many settings with covariate measurement error, it is biased for nonlinear regression models, such as the Cox model. Thus, we additionally propose raking estimators which are consistent estimators of the parameter defined by the population estimating equations, can improve upon RC in certain settings with failure-time data, require no explicit modeling of the error structure, and can be utilized under outcome-dependent sampling designs. We discuss features of the underlying estimation problem that affect the degree of improvement the raking estimator has over the RC approach. Detailed simulation studies are presented to examine the performance of the proposed estimators under varying levels of signal, error, and censoring. The methodology is illustrated on observational EHR data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic. …

Gated Path Planning Network google
Value Iteration Networks (VINs) are effective differentiable path planning modules that can be used by agents to perform navigation while still maintaining end-to-end differentiability of the entire architecture. Despite their effectiveness, they suffer from several disadvantages including training instability, random seed sensitivity, and other optimization problems. In this work, we reframe VINs as recurrent-convolutional networks which demonstrates that VINs couple recurrent convolutions with an unconventional max-pooling activation. From this perspective, we argue that standard gated recurrent update equations could potentially alleviate the optimization issues plaguing VIN. The resulting architecture, which we call the Gated Path Planning Network, is shown to empirically outperform VIN on a variety of metrics such as learning speed, hyperparameter sensitivity, iteration count, and even generalization. Furthermore, we show that this performance gap is consistent across different maze transition types, maze sizes and even show success on a challenging 3D environment, where the planner is only provided with first-person RGB images. …

Pool Adjacent Violators Algorithm (PAVA) google
Pool Adjacent Violators Algorithm (PAVA) is a linear time (and linear memory) algorithm for linear ordering isotonic regression.
“Isotonic Regression”

DeepSSM google
Statistical shape modeling is an important tool to characterize variation in anatomical morphology. Typical shapes of interest are measured using 3D imaging and a subsequent pipeline of registration, segmentation, and some extraction of shape features or projections onto some lower-dimensional shape space, which facilitates subsequent statistical analysis. Many methods for constructing compact shape representations have been proposed, but are often impractical due to the sequence of image preprocessing operations, which involve significant parameter tuning, manual delineation, and/or quality control by the users. We propose DeepSSM: a deep learning approach to extract a low-dimensional shape representation directly from 3D images, requiring virtually no parameter tuning or user assistance. DeepSSM uses a convolutional neural network (CNN) that simultaneously localizes the biological structure of interest, establishes correspondences, and projects these points onto a low-dimensional shape representation in the form of PCA loadings within a point distribution model. To overcome the challenge of the limited availability of training images, we present a novel data augmentation procedure that uses existing correspondences on a relatively small set of processed images with shape statistics to create plausible training samples with known shape parameters. Hence, we leverage the limited CT/MRI scans (40-50) into thousands of images needed to train a CNN. After the training, the CNN automatically produces accurate low-dimensional shape representations for unseen images. We validate DeepSSM for three different applications pertaining to modeling pediatric cranial CT for characterization of metopic craniosynostosis, femur CT scans identifying morphologic deformities of the hip due to femoroacetabular impingement, and left atrium MRI scans for atrial fibrillation recurrence prediction. …